Spud DB is a collection of datasets and data-mining tools to view and analyze the potato genome, including tools to facilitate breeding improved cultivars.
Potato (Solanum tuberosum L.) is the fourth most important crop in the world, behind wheat, rice, and maize. In 2004, worldwide potato production exceeded 327 million metric tons. Potato also produces more food energy and value per unit of land area than any other crop. Compared to grain crops, potato is a superior source of nutrition; however, among major crop plants, potato is arguably the most intensively managed. In addition, tuber quality requirements are complex and must be maintained during harvest and storage. The genome sequence of potato was released and published in 2011 by the International Potato Genome Sequencing Consortium (PGSC). The assembled potato genome is that of the doubled monoploid S. tuberosum Group Phureja DM1-3 (DM; AEWC00000000); the genome assembly represents 726 MB, of which 86%, is anchored to the genetic map and contains 39,031 annotated genes. In addition, BAC and whole genome shotgun sequences were released from a second clone, S. tuberosum Group Tuberosum RH89-039-16 (RH; ERP000627).
Spud DB houses potato genome browsers for the newly released version PGSC v4.03 pseudomolecules and for the previous PGSC v2.1.11 pseudomolecule release. The browsers contain information for the PGSC and the International Tomato Annnotation Group (ITAG) loci, hits to Arabidopsis, grape, poplar, tomato, and PlantGDB transcript assemblies for 12 other Solanaceae species. The potato genome browsers also contain data from 56 RNA-Seq libraries from DM (SRA030516) and RH (ERP000527), and SolCAP SNP information (Hamilton et al. 2011) (Felcher et al. 2012).
Each transcript annotated by the PGSC and the ITAG groups has a transcript report page that displays transcript and predicted protein sequences along with matches to UniRef, InterPro, Arabidopsis, tomato, and other potato sequences. Information is also available for SSRs, SNPs, and expression (FPKM) values in 56 tissues for the sequence.
Through the SolCAP project, resources focused on translating genomic advances in potato to US breeding programs. We developed 'Breeder's Assistant' tools to provide easy and quick access to potato genotypic and phenotypic data. The tools currently focus on the SolCAP potato 8303 SNP Infinium array (Hamilton et al. 2011) (Felcher et al. 2012) and the data generated by a 250 clone diversity panel (Hirsch et al. 2013)
We welcome input from outside researchers. If there is some way in which we can improve this resource, we would like to hear from you. Please use the comment form on our contact page to send us your suggestions.
Funding has been provided by awards from the U.S. Department of Agriculture (2008-35300-18671) and the U.S. National Science Foundation (DBI-0604907, DBI-0834044, and 1202724). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
An update has been made to the Breeder's Assistant Tools. Searching for SNPs via gene annotation is no longer case sensitive, leading to more complete search results.
A paper describing the resources, tools and data available in Spud DB has been published in the journal The Plant Genome.
The DM and RH RNA-Seq FPKM summary files were regenerated with the corrected PGSC DM v4.03 Pseudomolecule annotation. Please see the PGSC Data Download Page for more information.
The PGSC DM v4.03 Pseudomolecule GFF Files have been updated to correct an error. Please see the PGSC Data Download Page for more information.
A paper describing the construction of the PGSC v4.03 pseudomolecules for S. tuberosum Group Phureja DM1-3 has been published in the journal G3: Genes, Genomes, Genetics. The new pseudomolecules can be downloaded from the PGSC Data Download Page
We have planned server maintenance on the first Wednesday of every month and therefore, Spud DB web pages may be unavailable or only partially functional during server maintenance. Spud DB will also not be available December 2, 2013 and April 7, 2014 due to additional maintenance.